Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.
References
[1]
Dunham, I.; Kundaje, A.; Aldred, S.F.; Collins, P.J.; Davis, C.A.; Doyle, F.; Epstein, C.B.; Frietze, S.; Harrow, J.; Kaul, R.; et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489, 57–74.
[2]
Sastre, L. Clinical implications of the encode project. Clin. Transl. Oncol. 2012, 14, 801–802, doi:10.1007/s12094-012-0958-0.
[3]
Frazer, K.A. Decoding the human genome. Genome Res. 2012, 22, 1599–1601, doi:10.1101/gr.146175.112.
[4]
Database of Genomic Variants. Available online: http://projects.tcag.ca/ (accessed on 5 July 2012).
Sanger, F.; Nicklen, S.; Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977, 74, 5463–5467, doi:10.1073/pnas.74.12.5463.
[7]
Sanger, F.; Coulson, A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 1975, 94, 441–448, doi:10.1016/0022-2836(75)90213-2.
[8]
Liu, L.; Li, Y.; Li, S.; Hu, N.; He, Y.; Pong, R.; Lin, D.; Lu, L.; Law, M. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 2012, 251364.
[9]
Genomeweb. Available online: http://genomeweb.com/ (accessed on 12 December 2012).
[10]
Schadt, E.E.; Turner, S.; Kasarskis, A. A window into third-generation sequencing. Hum. Mol. Genet. 2010, 19, R227–R240, doi:10.1093/hmg/ddq416.
[11]
Braslavsky, I.; Hebert, B.; Kartalov, E.; Quake, S.R. Sequence information can be obtained from single DNA molecules. Proc. Natl. Acad. Sci. USA 2003, 100, 3960–3964.
[12]
Pareek, C.S.; Smoczynski, R.; Tretyn, A. Sequencing technologies and genome sequencing. J. Appl. Genet. 2011, 52, 413–435, doi:10.1007/s13353-011-0057-x.
[13]
Astier, Y.; Braha, O.; Bayley, H. Toward single molecule DNA sequencing: Direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J. Am. Chem. Soc. 2006, 128, 1705–1710, doi:10.1021/ja057123+.
[14]
Rusk, N. Focus on next-generation sequencing data analysis. Nat. Methods 2009, 6, S1, doi:10.1038/nmeth.f.271.
[15]
Lee, H.C.; Lai, K.; Lorenc, M.T.; Imelfort, M.; Duran, C.; Edwards, D. Bioinformatics tools and databases for analysis of next-generation sequence data. Brief Funct. Genomics 2012, 11, 12–24, doi:10.1093/bfgp/elr037.
[16]
Torri, F.; Dinov, I.D.; Zamanyan, A.; Hobel, S.; Genco, A.; Petrosyan, P.; Clark, A.P.; Liu, Z.; Eggert, P.; Pierce, J.; et al. Next generation sequence analysis and computational genomics using graphical pipeline workflows. Genes 2012, 3, 545–575, doi:10.3390/genes3030545.
[17]
Afgan, E.; Chapman, B.; Taylor, J. Cloudman as a platform for tool, data, and analysis distribution. BMC Bioinformatics 2012, 13, 315, doi:10.1186/1471-2105-13-315.
[18]
Schadt, E.E.; Linderman, M.D.; Sorenson, J.; Lee, L.; Nolan, G.P. Computational solutions to large-scale data management and analysis. Nat. Rev. Genet. 2010, 11, 647–657.
[19]
Abeel, T.; van Parys, T.; Saeys, Y.; Galagan, J.; van de Peer, Y. Genomeview: A next-generation genome browser. Nucleic Acids Res. 2012, 40, e12, doi:10.1093/nar/gkr995.
[20]
Bao, S.; Jiang, R.; Kwan, W.; Wang, B.; Ma, X.; Song, Y.Q. Evaluation of next-generation sequencing software in mapping and assembly. J. Hum. Genet. 2011, 56, 406–414, doi:10.1038/jhg.2011.43.
[21]
Cordero, F.; Beccuti, M.; Donatelli, S.; Calogero, R.A. Large disclosing the nature of computational tools for the analysis of next generation sequencing data. Curr. Top. Med. Chem. 2012, 12, 1320–1330, doi:10.2174/156802612801319007.
[22]
Hershberger, R.E.; Siegfried, J.D. Update 2011: Clinical and genetic issues in familial dilated cardiomyopathy. J. Am. Coll Cardiol. 2011, 57, 1641–1649, doi:10.1016/j.jacc.2011.01.015.
[23]
Bamshad, M.J.; Ng, S.B.; Bigham, A.W.; Tabor, H.K.; Emond, M.J.; Nickerson, D.A.; Shendure, J. Exome sequencing as a tool for mendelian disease gene discovery. Nat. Rev. Genet. 2011, 12, 745–755, doi:10.1038/nrg3031.
[24]
Ng, S.B.; Buckingham, K.J.; Lee, C.; Bigham, A.W.; Tabor, H.K.; Dent, K.M.; Huff, C.D.; Shannon, P.T.; Jabs, E.W.; Nickerson, D.A.; et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 2010, 42, 30–35.
[25]
Ng, S.B.; Turner, E.H.; Robertson, P.D.; Flygare, S.D.; Bigham, A.W.; Lee, C.; Shaffer, T.; Wong, M.; Bhattacharjee, A.; Eichler, E.E.; et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009, 461, 272–276.
[26]
Hood, R.L.; Lines, M.A.; Nikkel, S.M.; Schwartzentruber, J.; Beaulieu, C.; Nowaczyk, M.J.; Allanson, J.; Kim, C.A.; Wieczorek, D.; Moilanen, J.S.; et al. Mutations in srcap, encoding snf2-related crebbp activator protein, cause floating-harbor syndrome. Am. J. Hum. Genet. 2012, 90, 308–313, doi:10.1016/j.ajhg.2011.12.001.
[27]
Ng, S.B.; Bigham, A.W.; Buckingham, K.J.; Hannibal, M.C.; McMillin, M.J.; Gildersleeve, H.I.; Beck, A.E.; Tabor, H.K.; Cooper, G.M.; Mefford, H.C.; et al. Exome sequencing identifies mll2 mutations as a cause of kabuki syndrome. Nat. Genet. 2010, 42, 790–793.
[28]
Wang, J.L.; Yang, X.; Xia, K.; Hu, Z.M.; Weng, L.; Jin, X.; Jiang, H.; Zhang, P.; Shen, L.; Guo, J.F.; et al. Tgm6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain 2010, 133, 3510–3518, doi:10.1093/brain/awq323.
[29]
Tariq, M.; Belmont, J.W.; Lalani, S.; Smolarek, T.; Ware, S.M. Shroom3 is a novel candidate for heterotaxy identified by whole exome sequencing. Genome Biol. 2011, 12, R91, doi:10.1186/gb-2011-12-9-r91.
[30]
Lara-Pezzi, E.; Dopazo, A.; Manzanares, M. Understanding cardiovascular disease: A journey through the genome (and what we found there). Dis. Model Mech. 2012, 5, 434–443, doi:10.1242/dmm.009787.
[31]
Musunuru, K.; Pirruccello, J.P.; Do, R.; Peloso, G.M.; Guiducci, C.; Sougnez, C.; Garimella, K.V.; Fisher, S.; Abreu, J.; Barry, A.J.; et al. Exome sequencing, angptl3 mutations, and familial combined hypolipidemia. N. Engl. J. Med. 2010, 363, 2220–2227.
[32]
Meder, B.; Haas, J.; Keller, A.; Heid, C.; Just, S.; Borries, A.; Boisguerin, V.; Scharfenberger-Schmeer, M.; Stahler, P.; Beier, M.; et al. Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies. Circ. Cardiovasc. Genet. 2011, 4, 110–122, doi:10.1161/CIRCGENETICS.110.958322.
[33]
Herman, D.S.; Lam, L.; Taylor, M.R.; Wang, L.; Teekakirikul, P.; Christodoulou, D.; Conner, L.; DePalma, S.R.; McDonough, B.; Sparks, E.; et al. Truncations of titin causing dilated cardiomyopathy. N. Engl. J. Med. 2012, 366, 619–628.
[34]
Gerull, B.; Gramlich, M.; Atherton, J.; McNabb, M.; Trombitas, K.; Sasse-Klaassen, S.; Seidman, J.G.; Seidman, C.; Granzier, H.; Labeit, S.; et al. Mutations of ttn, encoding the giant muscle filament titin, cause familial dilated cardiomyopathy. Nat. Genet. 2002, 30, 201–204.
Norton, N.; Li, D.; Rieder, M.J.; Siegfried, J.D.; Rampersaud, E.; Zuchner, S.; Mangos, S.; Gonzalez-Quintana, J.; Wang, L.; McGee, S.; et al. Genome-wide studies of copy number variation and exome sequencing identify rare variants in bag3 as a cause of dilated cardiomyopathy. Am. J. Hum. Genet. 2011, 88, 273–282, doi:10.1016/j.ajhg.2011.01.016.
[37]
Clark, M.J.; Chen, R.; Lam, H.Y.; Karczewski, K.J.; Euskirchen, G.; Butte, A.J.; Snyder, M. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 2011, 29, 908–914.
Meyerson, M.; Gabriel, S.; Getz, G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 2010, 11, 685–696, doi:10.1038/nrg2841.
[40]
Lupski, J.R.; Reid, J.G.; Gonzaga-Jauregui, C.; Rio Deiros, D.; Chen, D.C.; Nazareth, L.; Bainbridge, M.; Dinh, H.; Jing, C.; Wheeler, D.A.; et al. Whole-genome sequencing in a patient with charcot-marie-tooth neuropathy. N. Engl. J. Med. 2010, 362, 1181–1191, doi:10.1056/NEJMoa0908094.
[41]
Smith, K.A.; Joziasse, I.C.; Chocron, S.; van Dinther, M.; Guryev, V.; Verhoeven, M.C.; Rehmann, H.; van der Smagt, J.J.; Doevendans, P.A.; Cuppen, E.; et al. Dominant-negative alk2 allele associates with congenital heart defects. Circulation 2009, 119, 3062–3069.
[42]
Meder, B.; Laufer, C.; Hassel, D.; Just, S.; Marquart, S.; Vogel, B.; Hess, A.; Fishman, M.C.; Katus, H.A.; Rottbauer, W. A single serine in the carboxyl terminus of cardiac essential myosin light chain-1 controls cardiomyocyte contractility in vivo. Circ. Res. 2009, 104, 650–659, doi:10.1161/CIRCRESAHA.108.186676.
[43]
Pan, Q.; Shai, O.; Lee, L.J.; Frey, B.J.; Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 40, 1413–1415.
[44]
Wang, G.S.; Cooper, T.A. Splicing in disease: Disruption of the splicing code and the decoding machinery. Nat. Rev. Genet. 2007, 8, 749–761.
[45]
Chacko, E.; Ranganathan, S. Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse. BMC Genomics 2009, 10, S5.
[46]
Modrek, B.; Lee, C. A genomic view of alternative splicing. Nat. Genet. 2002, 30, 13–19, doi:10.1038/ng0102-13.
[47]
Matlin, A.J.; Clark, F.; Smith, C.W. Understanding alternative splicing: Towards a cellular code. Nat. Rev. Mol. Cell Biol. 2005, 6, 386–398.
[48]
Bentley, D. Coupling rna polymerase ii transcription with pre-mRNA processing. Curr. Opin. Cell Biol. 1999, 11, 347–351.
[49]
Minvielle-Sebastia, L.; Keller, W. mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription. Curr. Opin. Cell Biol. 1999, 11, 352–357, doi:10.1016/S0955-0674(99)80049-0.
[50]
Maniatis, T.; Reed, R. An extensive network of coupling among gene expression machines. Nature 2002, 416, 499–506.
[51]
Philips, A.V.; Cooper, T.A. RNA processing and human disease. Cell. Mol. Life Sci. 2000, 57, 235–249, doi:10.1007/PL00000687.
[52]
Stoss, O.; Olbrich, M.; Hartmann, A.M.; Konig, H.; Memmott, J.; Andreadis, A.; Stamm, S. The star/gsg family protein rslm-2 regulates the selection of alternative splice sites. J. Biol. Chem. 2001, 276, 8665–8673.
[53]
Jensen, K.B.; Dredge, B.K.; Stefani, G.; Zhong, R.; Buckanovich, R.J.; Okano, H.J.; Yang, Y.Y.; Darnell, R.B. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 2000, 25, 359–371, doi:10.1016/S0896-6273(00)80900-9.
[54]
Mendell, J.T.; Dietz, H.C. When the message goes awry: Disease-producing mutations that influence mrna content and performance. Cell 2001, 107, 411–414, doi:10.1016/S0092-8674(01)00583-9.
[55]
Caceres, J.F.; Kornblihtt, A.R. Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Genet. 2002, 18, 186–193, doi:10.1016/S0168-9525(01)02626-9.
[56]
Nissim-Rafinia, M.; Kerem, B. Splicing regulation as a potential genetic modifier. Trends Genet. 2002, 18, 123–127, doi:10.1016/S0168-9525(01)02619-1.
[57]
Faustino, N.A.; Cooper, T.A. Pre-mRNA splicing and human disease. Genes Dev. 2003, 17, 419–437, doi:10.1101/gad.1048803.
[58]
Cooper, T.A.; Wan, L.; Dreyfuss, G. RNA and disease. Cell 2009, 136, 777–793, doi:10.1016/j.cell.2009.02.011.
[59]
Venables, J.P. Aberrant and alternative splicing in cancer. Cancer Res. 2004, 64, 7647–7654, doi:10.1158/0008-5472.CAN-04-1910.
Tang, F.; Lao, K.; Surani, M.A. Development and applications of single-cell transcriptome analysis. Nat. Methods 2011, 8, S6–S11.
[62]
Wang, Z.; Gerstein, M.; Snyder, M. RNA-seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57–63, doi:10.1038/nrg2484.
[63]
Raghavachari, N.; Barb, J.; Yang, Y.; Liu, P.; Woodhouse, K.; Levy, D.; O'Donnell, C.J.; Munson, P.J.; Kato, G.J. A systematic comparison and evaluation of high density exon arrays and rna-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease. BMC Med. Genomics 2012, 5, 28.
[64]
Feng, J.; Li, W.; Jiang, T. Inference of isoforms from short sequence reads. J. Comput. Biol. 2011, 18, 305–321, doi:10.1089/cmb.2010.0243.
[65]
Marioni, J.C.; Mason, C.E.; Mane, S.M.; Stephens, M.; Gilad, Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18, 1509–1517, doi:10.1101/gr.079558.108.
[66]
Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320, 1344–1349.
[67]
Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.; et al. Full-length transcriptome assembly from rna-seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644–652.
[68]
Herbert, A.; Rich, A. RNA processing in evolution. The logic of soft-wired genomes. Ann. N. Y. Acad. Sci. 1999, 870, 119–132, doi:10.1111/j.1749-6632.1999.tb08872.x.
[69]
Kwan, T.; Benovoy, D.; Dias, C.; Gurd, S.; Serre, D.; Zuzan, H.; Clark, T.A.; Schweitzer, A.; Staples, M.K.; Wang, H.; et al. Heritability of alternative splicing in the human genome. Genome Res. 2007, 17, 1210–1218, doi:10.1101/gr.6281007.
[70]
Cheung, V.G.; Spielman, R.S.; Ewens, K.G.; Weber, T.M.; Morley, M.; Burdick, J.T. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005, 437, 1365–1369.
[71]
Veyrieras, J.B.; Kudaravalli, S.; Kim, S.Y.; Dermitzakis, E.T.; Gilad, Y.; Stephens, M.; Pritchard, J.K. High-resolution mapping of expression-qtls yields insight into human gene regulation. PLoS Genet. 2008, 4, e1000214.
Tang, F.; Barbacioru, C.; Wang, Y.; Nordman, E.; Lee, C.; Xu, N.; Wang, X.; Bodeau, J.; Tuch, B.B.; Siddiqui, A.; et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 2009, 6, 377–382.
[74]
Wang, E.T.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S.F.; Schroth, G.P.; Burge, C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456, 470–476.
[75]
Backes, C.; Meese, E.; Lenhof, H.P.; Keller, A. A dictionary on micrornas and their putative target pathways. Nucleic Acids Res. 2010, 38, 4476–4486.
[76]
David, C.J.; Manley, J.L. Alternative pre-mRNA splicing regulation in cancer: Pathways and programs unhinged. Genes Dev. 2010, 24, 2343–2364, doi:10.1101/gad.1973010.
[77]
Biesiadecki, B.J.; Elder, B.D.; Yu, Z.B.; Jin, J.P. Cardiac troponin t variants produced by aberrant splicing of multiple exons in animals with high instances of dilated cardiomyopathy. J. Biol. Chem. 2002, 277, 50275–50285, doi:10.1074/jbc.M206369200.
[78]
Neagoe, C.; Kulke, M.; del Monte, F.; Gwathmey, J.K.; de Tombe, P.P.; Hajjar, R.J.; Linke, W.A. Titin isoform switch in ischemic human heart disease. Circulation 2002, 106, 1333–1341.
[79]
Philips, A.V.; Timchenko, L.T.; Cooper, T.A. Disruption of splicing regulated by a cug-binding protein in myotonic dystrophy. Science 1998, 280, 737–741, doi:10.1126/science.280.5364.737.
[80]
Poon, K.L.; Tan, K.T.; Wei, Y.Y.; Ng, C.P.; Colman, A.; Korzh, V.; Xu, X.Q. RNA-binding protein rbm24 is required for sarcomere assembly and heart contractility. Cardiovasc. Res. 2012, 94, 418–427, doi:10.1093/cvr/cvs095.
[81]
Refaat, M.M.; Lubitz, S.A.; Makino, S.; Islam, Z.; Frangiskakis, J.M.; Mehdi, H.; Gutmann, R.; Zhang, M.L.; Bloom, H.L.; MacRae, C.A.; et al. Genetic variation in the alternative splicing regulator rbm20 is associated with dilated cardiomyopathy. Heart Rhythm. 2012, 9, 390–396.
[82]
Brauch, K.M.; Karst, M.L.; Herron, K.J.; de Andrade, M.; Pellikka, P.A.; Rodeheffer, R.J.; Michels, V.V.; Olson, T.M. Mutations in ribonucleic acid binding protein gene cause familial dilated cardiomyopathy. J. Am. Coll Cardiol. 2009, 54, 930–941.
[83]
Guo, W.; Schafer, S.; Greaser, M.L.; Radke, M.H.; Liss, M.; Govindarajan, T.; Maatz, H.; Schulz, H.; Li, S.; Parrish, A.M.; et al. Rbm20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nat. Med. 2012, 18, 766–773.
[84]
Bass, B.L. RNA editing and hypermutation by adenosine deamination. Trends Biochem. Sci. 1997, 22, 157–162, doi:10.1016/S0968-0004(97)01035-9.
[85]
Maas, S.; Patt, S.; Schrey, M.; Rich, A. Underediting of glutamate receptor glur-b mrna in malignant gliomas. Proc. Natl. Acad. Sci. USA 2001, 98, 14687–14692.
[86]
Patterson, J.B.; Samuel, C.E. Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: Evidence for two forms of the deaminase. Mol. Cell Biol. 1995, 15, 5376–5388.
[87]
Kawahara, Y.; Ito, K.; Sun, H.; Aizawa, H.; Kanazawa, I.; Kwak, S. Glutamate receptors: RNA editing and death of motor neurons. Nature 2004, 427, 801.
Seeburg, P.H.; Higuchi, M.; Sprengel, R. RNA editing of brain glutamate receptor channels: Mechanism and physiology. Brain Res. Brain Res. Rev. 1998, 26, 217–229, doi:10.1016/S0165-0173(97)00062-3.
[90]
Athanasiadis, A.; Rich, A.; Maas, S. Widespread a-to-i RNA editing of alu-containing mrnas in the human transcriptome. PLoS Biol. 2004, 2, e391, doi:10.1371/journal.pbio.0020391.
[91]
Levanon, E.Y.; Eisenberg, E.; Yelin, R.; Nemzer, S.; Hallegger, M.; Shemesh, R.; Fligelman, Z.Y.; Shoshan, A.; Pollock, S.R.; Sztybel, D.; et al. Systematic identification of abundant a-to-i editing sites in the human transcriptome. Nat. Biotechnol. 2004, 22, 1001–1005.
[92]
Birney, E.; Stamatoyannopoulos, J.A.; Dutta, A.; Guigo, R.; Gingeras, T.R.; Margulies, E.H.; Weng, Z.; Snyder, M.; Dermitzakis, E.T.; Thurman, R.E.; et al. Identification and analysis of functional elements in 1% of the human genome by the encode pilot project. Nature 2007, 447, 799–816.
Mattick, J.S. Non-coding RNAs: The architects of eukaryotic complexity. EMBO Rep. 2001, 2, 986–991, doi:10.1093/embo-reports/kve230.
[95]
Pang, K.C.; Frith, M.C.; Mattick, J.S. Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function. Trends Genet. 2006, 22, 1–5, doi:10.1016/j.tig.2005.10.003.
[96]
Costa, V.; Angelini, C.; de Feis, I.; Ciccodicola, A. Uncovering the complexity of transcriptomes with RNA-seq. J. Biomed. Biotechnol. 2010, 2010, 853916.
[97]
Fratkin, E.; Bercovici, S.; Stephan, D.A. The implications of encode for diagnostics. Nat. Biotechnol. 2012, 30, 1064–1065.
[98]
Tilgner, H.; Knowles, D.G.; Johnson, R.; Davis, C.A.; Chakrabortty, S.; Djebali, S.; Curado, J.; Snyder, M.; Gingeras, T.R.; Guigo, R. Deep sequencing of subcellular rna fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncrnas. Genome Res. 2012, 22, 1616–1625, doi:10.1101/gr.134445.111.
Mattick, J.S.; Amaral, P.P.; Dinger, M.E.; Mercer, T.R.; Mehler, M.F. RNA regulation of epigenetic processes. Bioessays 2009, 31, 51–59, doi:10.1002/bies.080099.
[101]
Mattick, J.S. The genetic signatures of noncoding rnas. PLoS Genet. 2009, 5, e1000459, doi:10.1371/journal.pgen.1000459.
[102]
Derrien, T.; Johnson, R.; Bussotti, G.; Tanzer, A.; Djebali, S.; Tilgner, H.; Guernec, G.; Martin, D.; Merkel, A.; Knowles, D.G.; et al. The gencode v7 catalog of human long noncoding rnas: Analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22, 1775–1789, doi:10.1101/gr.132159.111.
[103]
Struhl, K. Transcriptional noise and the fidelity of initiation by rna polymerase II. Nat. Struct. Mol. Biol. 2007, 14, 103–105, doi:10.1038/nsmb0207-103.
[104]
Taft, R.J.; Pang, K.C.; Mercer, T.R.; Dinger, M.; Mattick, J.S. Non-coding RNAs: Regulators of disease. J. Pathol. 2010, 220, 126–139, doi:10.1002/path.2638.
[105]
Orom, U.A.; Derrien, T.; Guigo, R.; Shiekhattar, R. Long noncoding rnas as enhancers of gene expression. Cold Spring Harb. Symp. Quant. Biol. 2010, 75, 325–331, doi:10.1101/sqb.2010.75.058.
[106]
Orom, U.A.; Derrien, T.; Beringer, M.; Gumireddy, K.; Gardini, A.; Bussotti, G.; Lai, F.; Zytnicki, M.; Notredame, C.; Huang, Q.; et al. Long noncoding rnas with enhancer-like function in human cells. Cell 2010, 143, 46–58, doi:10.1016/j.cell.2010.09.001.
[107]
Hung, T.; Wang, Y.; Lin, M.F.; Koegel, A.K.; Kotake, Y.; Grant, G.D.; Horlings, H.M.; Shah, N.; Umbricht, C.; Wang, P.; et al. Extensive and coordinated transcription of noncoding rnas within cell-cycle promoters. Nat. Genet. 2011, 43, 621–629.
[108]
Huarte, M.; Guttman, M.; Feldser, D.; Garber, M.; Koziol, M.J.; Kenzelmann-Broz, D.; Khalil, A.M.; Zuk, O.; Amit, I.; Rabani, M.; et al. A large intergenic noncoding rna induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142, 409–419, doi:10.1016/j.cell.2010.06.040.
[109]
Christov, C.P.; Trivier, E.; Krude, T. Noncoding human y RNAs are overexpressed in tumours and required for cell proliferation. Br. J. Cancer 2008, 98, 981–988.
[110]
Angeloni, D.; ter Elst, A.; Wei, M.H.; van der Veen, A.Y.; Braga, E.A.; Klimov, E.A.; Timmer, T.; Korobeinikova, L.; Lerman, M.I.; Buys, C.H. Analysis of a new homozygous deletion in the tumor suppressor region at 3p12. 3 reveals two novel intronic noncoding rna genes. Genes Chromosomes Cancer 2006, 45, 676–691, doi:10.1002/gcc.20332.
[111]
Koob, M.D.; Moseley, M.L.; Schut, L.J.; Benzow, K.A.; Bird, T.D.; Day, J.W.; Ranum, L.P. An untranslated ctg expansion causes a novel form of spinocerebellar ataxia (sca8). Nat. Genet. 1999, 21, 379–384.
[112]
Lee, J.H.; Gao, C.; Peng, G.; Greer, C.; Ren, S.; Wang, Y.; Xiao, X. Analysis of transcriptome complexity through rna sequencing in normal and failing murine hearts. Circ. Res. 2011, 109, 1332–1341, doi:10.1161/CIRCRESAHA.111.249433.
Krol, J.; Loedige, I.; Filipowicz, W. The widespread regulation of microrna biogenesis, function and decay. Nat. Rev. Genet. 2010, 11, 597–610.
[118]
Ramsingh, G.; Koboldt, D.C.; Trissal, M.; Chiappinelli, K.B.; Wylie, T.; Koul, S.; Chang, L.W.; Nagarajan, R.; Fehniger, T.A.; Goodfellow, P.; et al. Complete characterization of the micrornaome in a patient with acute myeloid leukemia. Blood 2010, 116, 5316–5326.
[119]
Latronico, M.V.; Condorelli, G. Micrornas and cardiac pathology. Nat. Rev. Cardiol. 2009, 6, 419–429.
[120]
Calin, G.A.; Croce, C.M. Investigation of microrna alterations in leukemias and lymphomas. Methods Enzymol. 2007, 427, 193–213.
[121]
Keller, A.; Backes, C.; Leidinger, P.; Kefer, N.; Boisguerin, V.; Barbacioru, C.; Vogel, B.; Matzas, M.; Huwer, H.; Katus, H.A.; et al. Next-generation sequencing identifies novel micrornas in peripheral blood of lung cancer patients. Mol. Biosyst. 2011, 7, 3187–3199, doi:10.1039/c1mb05353a.
[122]
Keller, A.; Leidinger, P.; Bauer, A.; Elsharawy, A.; Haas, J.; Backes, C.; Wendschlag, A.; Giese, N.; Tjaden, C.; Ott, K.; et al. Toward the blood-borne mirnome of human diseases. Nat. Methods 2011, 8, 841–843.
[123]
Meder, B.; Keller, A.; Vogel, B.; Haas, J.; Sedaghat-Hamedani, F.; Kayvanpour, E.; Just, S.; Borries, A.; Rudloff, J.; Leidinger, P.; et al. Microrna signatures in total peripheral blood as novel biomarkers for acute myocardial infarction. Basic Res. Cardiol. 2011, 106, 13–23.
[124]
Calin, G.A.; Pekarsky, Y.; Croce, C.M. The role of microrna and other non-coding RNA in the pathogenesis of chronic lymphocytic leukemia. Best Pract. Res. Clin. Haematol. 2007, 20, 425–437, doi:10.1016/j.beha.2007.02.003.
[125]
Calin, G.A.; Liu, C.G.; Ferracin, M.; Hyslop, T.; Spizzo, R.; Sevignani, C.; Fabbri, M.; Cimmino, A.; Lee, E.J.; Wojcik, S.E.; et al. Ultraconserved regions encoding ncrnas are altered in human leukemias and carcinomas. Cancer Cell 2007, 12, 215–229, doi:10.1016/j.ccr.2007.07.027.
[126]
Rossi, S.; Sevignani, C.; Nnadi, S.C.; Siracusa, L.D.; Calin, G.A. Cancer-associated genomic regions (cagrs) and noncoding RNAs: Bioinformatics and therapeutic implications. Mamm. Genome 2008, 19, 526–540, doi:10.1007/s00335-008-9119-8.
[127]
Braconi, C.; Kogure, T.; Valeri, N.; Huang, N.; Nuovo, G.; Costinean, S.; Negrini, M.; Miotto, E.; Croce, C.M.; Patel, T. Microrna-29 can regulate expression of the long non-coding RNA gene meg3 in hepatocellular cancer. Oncogene 2011, 30, 4750–4756, doi:10.1038/onc.2011.193.
[128]
Jeggari, A.; Marks, D.S.; Larsson, E. Mircode: A map of putative microrna target sites in the long non-coding transcriptome. Bioinformatics 2012, 28, 2062–2063.
[129]
Chen, X.; Liang, H.; Zhang, C.Y.; Zen, K. Mirna regulates noncoding RNA: A noncanonical function model. Trends Biochem. Sci. 2012, 37, 457–459, doi:10.1016/j.tibs.2012.08.005.
[130]
Egger, G.; Liang, G.; Aparicio, A.; Jones, P.A. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004, 429, 457–463.
[131]
Robertson, K.D. DNA methylation and human disease. Nat. Rev. Genet. 2005, 6, 597–610, doi:10.1038/nrg1655.
Szyf, M. The role of DNA hypermethylation and demethylation in cancer and cancer therapy. Curr. Oncol. 2008, 15, 72–75, doi:10.3747/co.v15i2.210.
[134]
Szyf, M.; Pakneshan, P.; Rabbani, S.A. DNA methylation and breast cancer. Biochem. Pharmacol. 2004, 68, 1187–1197.
[135]
Banerjee, H.N.; Verma, M. Epigenetic mechanisms in cancer. Biomark Med. 2009, 3, 397–410, doi:10.2217/bmm.09.26.
[136]
Vinci, M.C.; Polvani, G.; Pesce, M. Epigenetic programming and risk: The birthplace of cardiovascular disease? Stem Cell Rev. 2012, doi:10.1007/s12015-012-9398-z.
Movassagh, M.; Choy, M.K.; Knowles, D.A.; Cordeddu, L.; Haider, S.; Down, T.; Siggens, L.; Vujic, A.; Simeoni, I.; Penkett, C.; et al. Distinct epigenomic features in end-stage failing human hearts. Circulation 2011, 124, 2411–2422.
[139]
Haas, J.; Frese, K.S.; Park, Y.J.; Keller, A.; Vogel, B.; Lindroth, A.M.; Weichenhan, D.; Franke, J.; Fischer, S.; Bauer, A.; et al. Alterations in cardiac DNA methylation in human dilated cardiomyopathy. EMBO Mol. Med. 2013, 5, 1–17.
[140]
Bjornsson, H.T.; Fallin, M.D.; Feinberg, A.P. An integrated epigenetic and genetic approach to common human disease. Trends Genet. 2004, 20, 350–358, doi:10.1016/j.tig.2004.06.009.
[141]
Leung, A.; Schones, D.E.; Natarajan, R. Using epigenetic mechanisms to understand the impact of common disease causing alleles. Curr. Opin. Immunol. 2012, 24, 558–563.
[142]
Hackenberg, M.; Barturen, G.; Oliver, J.L. Ngsmethdb: A database for next-generation sequencing single-cytosine-resolution DNA methylation data. Nucleic Acids Res. 2011, 39, D75–D79, doi:10.1093/nar/gkq942.
[143]
Ryu, H.J.; Kim do, Y.; Park, J.Y.; Chang, H.Y.; Lee, M.H.; Han, K.H.; Chon, C.Y.; Ahn, S.H. Clinical features and prognosis of hepatocellular carcinoma with respect to pre-s deletion and basal core promoter mutations of hepatitis b virus genotype c2. J. Med. Virol. 2011, 83, 2088–2095.
Jacinto, F.V.; Ballestar, E.; Esteller, M. Methyl-DNA immunoprecipitation (medip): Hunting down the DNA methylome. Biotechniques 2008, 44, 35, 37, 39 passim.
[151]
Yu, W.; Jin, C.; Lou, X.; Han, X.; Li, L.; He, Y.; Zhang, H.; Ma, K.; Zhu, J.; Cheng, L.; et al. Global analysis of DNA methylation by methyl-capture sequencing reveals epigenetic control of cisplatin resistance in ovarian cancer cell. PLoS One 2011, 6, e29450.
[152]
Farthing, C.R.; Ficz, G.; Ng, R.K.; Chan, C.F.; Andrews, S.; Dean, W.; Hemberger, M.; Reik, W. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet. 2008, 4, e1000116.
[153]
Dindot, S.V.; Person, R.; Strivens, M.; Garcia, R.; Beaudet, A.L. Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions. Genome Res. 2009, 19, 1374–1383, doi:10.1101/gr.089185.108.
[154]
Down, T.A.; Rakyan, V.K.; Turner, D.J.; Flicek, P.; Li, H.; Kulesha, E.; Graf, S.; Johnson, N.; Herrero, J.; Tomazou, E.M.; et al. A bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 2008, 26, 779–785.
[155]
Koga, Y.; Pelizzola, M.; Cheng, E.; Krauthammer, M.; Sznol, M.; Ariyan, S.; Narayan, D.; Molinaro, A.M.; Halaban, R.; Weissman, S.M. Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res. 2009, 19, 1462–1470, doi:10.1101/gr.091447.109.
[156]
Straussman, R.; Nejman, D.; Roberts, D.; Steinfeld, I.; Blum, B.; Benvenisty, N.; Simon, I.; Yakhini, Z.; Cedar, H. Developmental programming of cpg island methylation profiles in the human genome. Nat. Struct. Mol. Biol. 2009, 16, 564–571.
[157]
Weber, M.; Hellmann, I.; Stadler, M.B.; Ramos, L.; Paabo, S.; Rebhan, M.; Schubeler, D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 2007, 39, 457–466.
[158]
Taiwo, O.; Wilson, G.A.; Morris, T.; Seisenberger, S.; Reik, W.; Pearce, D.; Beck, S.; Butcher, L.M. Methylome analysis using medip-seq with low DNA concentrations. Nat. Protoc. 2012, 7, 617–636.
[159]
Weinmann, A.S.; Yan, P.S.; Oberley, M.J.; Huang, T.H.; Farnham, P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and cpg island microarray analysis. Genes Dev. 2002, 16, 235–244, doi:10.1101/gad.943102.
[160]
Ballestar, E.; Paz, M.F.; Valle, L.; Wei, S.; Fraga, M.F.; Espada, J.; Cigudosa, J.C.; Huang, T.H.; Esteller, M. Methyl-cpg binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J. 2003, 22, 6335–6345, doi:10.1093/emboj/cdg604.
[161]
Robertson, G.; Hirst, M.; Bainbridge, M.; Bilenky, M.; Zhao, Y.; Zeng, T.; Euskirchen, G.; Bernier, B.; Varhol, R.; Delaney, A.; et al. Genome-wide profiles of stat1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 2007, 4, 651–657.
[162]
Euskirchen, G.M.; Rozowsky, J.S.; Wei, C.L.; Lee, W.H.; Zhang, Z.D.; Hartman, S.; Emanuelsson, O.; Stolc, V.; Weissman, S.; Gerstein, M.B.; et al. Mapping of transcription factor binding regions in mammalian cells by chip: Comparison of array- and sequencing-based technologies. Genome Res. 2007, 17, 898–909, doi:10.1101/gr.5583007.
[163]
Neveling, K.; Collin, R.W.; Gilissen, C.; van Huet, R.A.; Visser, L.; Kwint, M.P.; Gijsen, S.J.; Zonneveld, M.N.; Wieskamp, N.; de Ligt, J.; et al. Next-generation genetic testing for retinitis pigmentosa. Hum. Mutat. 2012, 33, 963–972.
[164]
Fokstuen, S.; Munoz, A.; Melacini, P.; Iliceto, S.; Perrot, A.; Ozcelik, C.; Jeanrenaud, X.; Rieubland, C.; Farr, M.; Faber, L.; et al. Rapid detection of genetic variants in hypertrophic cardiomyopathy by custom DNA resequencing array in clinical practice. J. Med. Genet. 2011, 48, 572–576.
[165]
Worthey, E.A.; Mayer, A.N.; Syverson, G.D.; Helbling, D.; Bonacci, B.B.; Decker, B.; Serpe, J.M.; Dasu, T.; Tschannen, M.R.; Veith, R.L.; et al. Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011, 13, 255–262.
[166]
Chou, L.S.; Liu, C.S.; Boese, B.; Zhang, X.; Mao, R. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: Neurofibromatosis type 1 gene as a model. Clin. Chem. 2010, 56, 62–72, doi:10.1373/clinchem.2009.132639.
[167]
Vogel, B.; Keller, A.; Frese, K.; Kloos, W.; Kayvanpour, E.; Sedaghat-Hamedani, F.; Hassel, S.; Marquart, S.; Beier, M.; Giannitis, E.; et al. Refining diagnostic microrna signatures by whole-mirnome kinetic analysis in acute myocardial infarction. Clin. Chem. 2012, 59, 410–418.
[168]
Davies Thirty Groups Enter Clarity Clinical Genome Interpretation Challenge. Available online: http://genes.childrenshospital.org/ (accessed on 12 July 2012).
De Lecea, M.G.; Rossbach, M. Translational genomics in personalized medicine—Scientific challenges en route to clinical practice. HUGO J. 2012, 6, 2, doi:10.1186/1877-6566-6-2.
